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Release History

Release Notes

OEDocking 3.2.0

December 2015

Major Features

  • posit is now part of the OEDocking suite (a posit license is still required to run posit).
  • Improved posit‘s clash detection. posit now ignores on a per atom basis clashes with the protein that the crystallographic ligand also makes.
  • OpenMPI version 1.6 is now supported on all plafforms. The -mpi_np and -mpi_hostfile flags are now used to run fred, hybrid and posit and MPI mode. These new flags replace the oempirun script.
  • pdb2receptor now incoporates all of make_pose_receptor‘s functionality. make_pose_receptor has now been retired.
  • pdb2receptor now supports the identification and selection of a desired ligand in a protein-ligand complex.

Minor Features

Major Bug Fixes

  • make_receptor no longer routinely crashed under a Japanese version of Windows.
  • Fixed a bug where pdf’s generated by docking_report causes an error under Windows versions of Acrobat.

Minor Bug Fixes

  • Fixed an off by one error in hybrid‘s progress reporting of how many molecules have been docked.
  • Fixed a bug where fred, hybrid or posit could crash if given a protein structure with non-sensical atom states.

POSIT v3.1.0

June 2014

Major Features

  • The hybrid and fred algorithms have been incorporated into posit, the appropriate method is determined by analyzing the ligand to pose against the input receptors.
  • Multiprocessing has been enabled through the use of MPI, to speed calculations.
  • posit now supports a list of receptors files or .lst file as input. This overcomes command-line limitations for the number of receptors that can be used simultaneously.
  • Added a MEDIOCRE result rating for results between 33% and 50% probability.
  • Command line parameters have been simplified and updated to be compatible with the OEDocking Suite of tools. The following command-line options have been removed, see the documentation for full details.
    • outcomplexes
    • outreceptors
    • clashcomplexes
    • clashreceptors
    • alternatePoses
    • cleanupWithProtein
    • mcs
    • minInitialProbability
    • minInitialTanimotoCombo
    • minTanimotoCombo
    • probabilityStop
    • scatter
    • selectReceptorBy
    • strain

Major Bug Fixes

  • posit no longer automatically strips out incoming SDData fields.

Minor Bug Fixes

  • The default for the option -ignore_nitrogen_stereo has been changed to true to account for the nature of time-averaged crystallographic structures.

OEDocking 3.0.1

September 2012

Changes

The program dock_report has been renamed to DOCKING_REPORT.

The formatting of the DOCKING_REPORT has been significantly improved.

Improved the geometry detection for hydrogen bond protein constraints. These constraints should now be tighter.

New Features

The output of DOCKING_REPORT now includes

  • Added a protein interaction fingerprint to the docking_report.
  • XLogP
  • Polar surface area (PSA)

Bug Fixes

Fix bug where clash detection between hydrogen bonding groups was occasionally to strict.

POSIT v1.0.3

September 2012

Major Bug Fixes

  • Stereo isomer detection was not handling bridgeheads properly, this caused some non-stereo molecules to be identified as such.

POSIT v1.0.2

July 2012

Major Features

  • The optimizer has been enhanced to produce better aligned structures in certain cases.

Major Bug Fixes

  • A memory leak in the optimizer has been fixed, POSIT now properly handles large streams of molecules.
  • The -mcs flag has been turned off by default. In some cases, the mcs was taking far too long for no real benefit in pose prediction.

OEDocking 3.0.0

April 2012

Changes

The OEDocking 3.0.0 release is the first release of the OEDocking package, which is an upgrade of the previous FRED release packages. The OEDocking package includes FRED along with a suite of new docking tools.

As part of this OEDocking release the interface to FRED has been streamlined. Several functions of FRED have been split out into separate programs that are now part of the OEDocking suite, and several older features that have not proved to improve docking results (or in the worse case degrade docking results relative to the defaults) have been removed.

The features of FRED 2.2.5 that have been moved to separate utility programs in 3.0.0 are as follows

  • Receptor Creation

    Receptors are now created either with the MAKE_RECEPTOR GUI or the PDB2RECEPTOR, APOPDB2RECEPTOR or RECEPTOR_SETUP command-line programs. Existing receptors can now also be edited or modified with the MAKE_RECEPTOR GUI or RECEPTOR_TOOLBOX command line program. These programs are all included in the OEDocking distribution.

    Relevant flags removed from FRED:

    • -pro
    • -strip_water
    • -bound_ligand
    • -box
    • -addbox
    • -no_inner_contour
  • :ref:`hybrid<hybrid>` Docking*

    Hybrid docking is now available as a separate application, HYBRID, included in the OEDocking distribution.

  • Rescoring of poses

    The feature to rescore existing poses is now available in a separate application, SCOREPOSE, included in the OEDocking distribution.

The features of FRED 2.2.5 removed in 3.0.0 are as follows

  • Alternate Scoring Functions

    FRED now uses the improved Chemgauss4 scoring function. This scoring function has better virtual screening and pose prediction performance than any of the scoring functions available in FRED 2.2.5.

    Relevant flags removed from FRED:

    • -exhaustive_scoring
    • -opt
    • -shapegauss
    • -plp
    • -chemgauss2
    • -chemgauss3
    • -chemscore
    • -oechemscore
    • -screenscore
    • -cgo
    • -cgt
    • -zapbind
    • -consensus
    • -shapegauss_masc
    • -plp_masc
    • -chemgauss2_masc
    • -chemgauss3_masc
    • -chemscore_masc
    • -oechemscore_masc
    • -screenscore_masc
    • -cgo_masc
    • -cgt_masc
    • -zapbind_masc
    • -consensus_masc
    • -assign_ligand_charges
  • MASC

    Multiple Active Site Correction (MASC) was introduced in FRED 2.1 as a method of compensating for the size bias in scoring functions. This size bias arises in many scoring functions where the interaction terms are all favorable interactions, and thus larger molecules score better since they can make more interactions. Chemgauss4 (and Chemgauss3), however, has both favorable interactions (i.e., shape, hydrogen bonding and metal-chelator) and unfavorable interactions (i.e., desolvation and clash), and therefore does not have a significant size bias that necessitates the use of MASC.

    Relevant flags removed from FRED:

    • -reference_receptors
    • -no_masc_data
    • -recalculate_masc_data
    • -report_masc_failures
  • Consensus Pose Selection

    FRED 2.2.5 had slightly better pose prediction results when the best docked pose was selected using a consensus of three scoring function (Chemgauss3, Chemscore and PLP) rather than one (Chemgauss3). The new Chemgauss4 scoring function in the 3.0 release is not improved by this feature, which has therefore has been removed.

    Relevant flags removed from FRED:

    • -pose_select_weight_shapegauss
    • -pose_select_weight_plp
    • -pose_select_weight_chemgauss2
    • -pose_select_weight_chemgauss3
    • -pose_select_weight_chemscore
    • -pose_select_weight_oechemscore
    • -pose_select_weight_screenscore
    • -pose_select_weight_cgo
    • -pose_select_weight_cgt
  • MMFF Refinement

    Using this option in FRED 2.2.5 degraded the results for both pose prediction and virtual screening and significant increases the run time.

    Relevant flags removed from FRED:

    • -refine

New Features

  • Chemgauss4 scoring

    Improved hydrogen bond detection vs. Chemgauss3. Hydrogen bond network effects are also now accounted for.

  • Hybrid docking

    Dock using ligand and protein structural information simultaneously

  • MPI

    MPI is now supported on all platforms except Windows.

  • Docking Report

    Creates an Adobe PDF docked report for selected docked molecules.

  • Receptor tools

    Streamlines the receptor setup GUI, and also added several command line tools for setting up receptors.

Bug Fixes

  • Fixed a bug where large hitlists (> ~50,000) would result is very slow runtimes.
  • SD tag data on the input ligand is now retained.
  • Added an option to toggle hardware rendering in the make_receptor GUI application to correct Windows driver related 3D graphics issues.

FRED 2.2.5 Change Log

New Features

  • On Microsoft Windows platforms, the installer adds the ability to open command prompts that setup the user environment to run specific versions of FRED or the latest version of FRED.

Changes

  • FRED and FRED_RECEPTOR are now versioned and shipped together.

Bug Fixes

  • FRED licenser has been updated to work with licenses that expire past the year 2009.
  • The FRED licenser supports having the license file located in the users home directory.
  • SD files are now written with the 3D flag set.
  • Fixed issue where Fred could crash if -nodock is specified and the poses given to Fred to score are not within the receptor site.

FRED 2.2.4 Change Log

Bug Fixes

  • Fixed crash when -refine and -no_dock were used together.
  • Fixed crash when -clash_scale and a receptor without an inner contour is used.

FRED 2.2.3 Change Log

Bug Fixes

  • Fixed a bug when using two custom constraints that caused all molecules to fail to dock with a NoConstraintMatch code.

FRED 2.2.2 Change Log

Bug Fixes

  • Fixed a bug that causes the -pharm flag to be ignored.
  • Cleaned up minor formatting issue when informing the user that a warning log has been opened.

FRED 2.2.1 Change Log

New Features

  • Added support for OEB rotor offset compression when writing the MASC tagged version of the input database (provided the initial input database used rotor offset compression).
  • Chemscore’s, OEChemscores’s and Screenscores’s hydrogen bonding terms now only allow one hydrogen bond per hydrogen. Also prevented two hydroxyls from making both and acceptor-donor interaction and a donor-acceptor interaction.

Changes

  • Modified OEChemscore’s hydrogen bonding term to be more forgiving of non-ideal geometries. The range of geometries considered ideal is unchanged.
  • Corrected a deficiency in Chemgauss3 metal term and metal constraints. The metal chelator interaction function were picking up on some but not all of the allowable geometries for metal-chelator interactions.
  • Improved Chemscore’s, OEChemscore’s and Screenscore’s handling of rotatable hydrogens involved in hydrogen bonding by replacing the brute force torsion driving search for the optimal hydrogen position with an analytic solution for the best position.
  • Added a new flag “-no_masc_data_calc” which will prevent Fred from calculating MASC data for ligands. Any ligands that missing needed masc data will not be docked. The purpose of this flag is to prevent from from doing a lengthy MASC calculation when all but a handful of ligands have the required MASC data.
  • Extended initial list of atom types know to Chemgauss3. This should improve the startup speed of runs using Chemgauss3, by avoiding costly grid recalculations each time a new atom type is encountered. This change is only for speed, there is no change to the Chemgauss3 score value Fred calculates.
  • When using constraints fred now defaults to effectively using a -clash_scale value of 0.6 if the -clash_scale flag has not been set by the user. This helps eliminate unusually close protein-ligand contacts that can occasionally occur when constraints are used. The original behavior can be obtained by explicitly setting -clash_scale to 0. Runs without constraints are unaffected and behave as before.
  • Chemgauss2 is not longer used by default in the consensus pose stage of docking. This has no real effect on docking performance and will reduces Fred’s startup time.

Bug Fixes

  • Important: Fixed a bug when using -pro and -box to create a receptor that causes the inner contour to be set to an extremely small value. The resulting receptor would produce extremely poor docking results without warning. In this release newly created receptors will now have reasonable inner contours. Additionally Fred now checks if the inner contour volume is extremely small (i.e., one that was produced by this bug), and if one is detected the inner contour is turned off and a warning is issued before proceeding with the run.
  • Fixed a when requesting alternate poses during a PVM run, which caused the run to shutdown and not dock any molecules.
  • Fixed a bug in screenscore when the receptor/protein it was initialized with did not have explicit hydrogens. The bug causes the initial setup to fail and the run to stop if screenscore was used. The error reported when this bug occurred was “Error! Screenscore::FindAcceptors (OH)”.
  • Fixed a crash bug when calculating MASC data for ligands on a 64bit machine.
  • Fixed minor when reporting how many molecules in a database have MASC data. The percentage reported was erroneously divided by 100.
  • Fixed a bug when using both the MASC and Non-MASC variants of a scoring function in the same run. The bug caused a shift in the Non-MASC score related to the precalculated MASC data, while the MASC variant score was correctly calculated. The error was especially damaging to CGT score.
  • Fixed spelling error by changing parameter -recalculate_masc_data to -recalculate_masc_data. The original misspelling is now an alias to minimize impact on users with existing parameter files.
  • Fixed bug checking for charges when -zapbind and -pro are used together. (Did not affect runs where -zapbind and -rec were being used). The bug caused the run to stop.
  • Fixed a bug in -clash_scale flag, that causes the value passed to the flag to be ignored and a value of one to be used. If the -clash_scale flag was not used no bug occurred in this regard.
  • Silenced the warning “OEInterface::Get, requesting value of unset parameter -addbox” when using the -box parameter without also specifying -addbox. The warning was spurious, no error occurred when it was issued.
  • Slave of a multiprocessor run now longer require a license, only the master process requires a license now.

Initial FRED 2.2 release

New Features / Improvements

Optional GUI setup and preparation of the active site (the actual docking remains command line). The GUI allows users to

  • Separate bound ligands and solvent molecules from the protein structure.
  • Detect active sites, and adjust the box defining the active site.
  • Manually tweak residue protonation states.
  • Visualize and adjust the complimentary shapes FRED uses during the exhaustive search.
  • Specify constraints.

A new version of the Chemgauss scoring function, version 3, which includes new desolvation terms as well as improved typing.

Ligand based design scoring functions, C.G.O (Chemical Gaussian Overlay) and C.G.T. (Chemical Gaussian Tanimoto). These functions score be measuring how well a molecules shape and chemistry overlay a known bound ligand placed in the active site.

All new algorithm for generating the negative image of the active site using molecular shape probes, as opposed to the atomic probes uses earlier.

On the fly preparation of MASC data for runs using the MASC variant scoring functions is now an option. Pre-calculating MASC data is still available and most efficient when doing multiple runs.

Changes

FRED now uses a special receptor file to describe the active site. This file can be created interactively using the new fred_receptor GUI program, or on the fly with the command line using the same flags as the previous version of FRED (2.1.x).

The functionality of the masc_prep and ligand_info programs distributed with the previous version (2.1.x) have been merged into the main fred executable.

Version 1 of Chemgauss has been removed, Version 2 is deprecated but still available.

Individual hitlist -size and -cut flags have be replaced by a single -hitlist_size flag.

POSIT v1.0.1

February 2012

Major Bug Fixes

  • In some rare cases the -mcs flag could cause a portion of the posed ligand to be fixed in space while the rest was optimized correctly, this causes very bad geometry molecules that can score very well. POSIT has been fixed to optimize the whole molecule in such cases.

Minor Bug Fixes

  • The version numbers for make_pose_receptor and combine_receptors were being incorrectly output in the OpenEye Banner, this has been updated to reflect the correct POSIT version.

Minor Features

  • -outputall flag has been added to send all computed output to the file specified by -out, -outcomplexes or -outreceptors. It as a shortcut for:

    -minInitialTanimotoCombo 0.0 -minTanimotoCombo 0.0 -minProbability 0.0 \
      -allowedClashes allclashes
    
  • if any of the input receptors has a clashing ligand, a warning will be output and POSIT will be set to accept clashes of the same severity as the receptor ligand.

  • POSIT can now stream output specified by the -out switch to stdout using the

    command line switch -out .sdf or -out .oeb

POSIT v1.0.0

November 2011

First release of POSIT.

Traditional structure based pose-prediction has not been very accurate in reproducing crystallographic poses. This can be rectified by using all of the information present in a crystal structure - both ligand and protein structure. POSIT is a flexible docking technique that uses both the known protein and ligand structure to predict poses. Furthermore, using this information generates a probability that the predicted pose is indeed correct. This has far reaching implications for real world lead optimization scenarios including measuring confidence but also the ability to select the existing crystal structure that best predicts the docked pose for a given molecule.

Features

  • Probability based pose-prediction
  • Performs better than structure-based pose-prediction for poses similar to known bound ligands.
  • All-atom optimization of poses based on known bound-ligands and ligand-protein interactions.
  • Fast detection of best known receptor (complex) to determine pose.